Alterations in the structural and functional states of chromatin, mainly determined by post-translational modification of histone components, are involved in the pathogenesis of a variety of diseases. These reversible modifications confer to the dynamicity of chromatin remodeling and are tightly controlled by the opposing activities of enzyme families. The enzymatic processes governing these post-translational modifications on the nucleosomes have become potential targets for the so-called epigenetic therapies (Portela, A. et al. Nat. Biotechnol. 2010, 28, 1057-1068).
The discovery of an increasing number of histone lysine demethylases has highlighted the dynamic nature of the regulation of histone methylation, a key chromatin modification that is involved in eukaryotic genome and gene regulation. Histone lysine demethylases represent attractive targets for epigenetic drugs, since their expression and/or activities are often misregulated in cancer (Varier, R. A. et al. Biochim. Biophys. Acta. 2011, 1815, 75-89). A lysine can be mono-, di-, and tri-methylated and each modification, even on the same amino acid, can exert different biological effects.
Histone lysine demethylases can be grouped into two major families with different enzymatic mechanisms (Anand, R. et al. J. Biol. Chem. 2007, 282, 35425-35429; Metzger, E. et al. Nat. Struct. Mol. Biol. 2007, 14, 252-254). On one side, we find the large protein family of Jumonji C (JmjC) domain-containing proteins, where the demethylation reaction is carried out by JmjC domain proteins and where a conserved JmjC domain, the presence of Fe(II) and α-ketoglutarate is required to generate formaldehyde and succinate and to allow the removal of mono-, di-, and trimethylated lysines. The demethylation reaction of the other class, which includes two proteins, is a flavin dependent oxidative process and is limited to mono- and di-methylated substrates. Mammals contain two flavin dependent amino oxidase histone lysine demethylases: KDM1A (also known as LSD1) and KDM1B (also known as LSD2). KDM1A is a constituent in several chromatin-remodeling complexes and is often associated with the co-repressor protein CoREST. It recruits in this form other histone modifying enzymes such as histone deacetylases 1/2 (HDAC1/2) forming a multienzyme unit typically involved in gene repression regulation (Ballas, N. et al. Neuron 2001, 31, 353-365). KDM1A specifically removes the methyl groups from both mono- and di-methyl Lys4 of histone H3, which is a well-characterized gene activation mark.
KDM1A represents an interesting target for epigenetic drugs as supported by data related to its over-expression in solid and hematological tumors (Schulte, J. H. et al. Cancer Res. 2009, 69, 2065-2071; Lim, S. et al. Carcinogenesis 2010, 31, 512-520; Hayami, S. et al. Int. J. Cancer 2011, 128, 574-586; Schildhaus, H. U. et al. Hum. Pathol. 2011, 42, 1667-1675; Bennani-Baiti, I. M. et al. Hum. Pathol. 2012, 43, 1300-1307), to the correlation of its over-expression and tumor recurrence in prostate cancer (Kahl, P. et al. Cancer Res. 2006, 66, 11341-11347), to its role in various differentiation processes as adipogenesis (Musri, M. M. et al. J. Biol. Chem. 2010, 285, 30034-30041), muscle skeletal differentiation (Choi, J. et al. Biochem. Biophys. Res. Commun. 2010, 401, 327-332), and hematopoiesis (Hu, X. et al. Proc. Natl. Acad. Sci. USA 2009, 106, 10141-10146; Li, Y. et al. Oncogene. 2012, 31, 5007-18), to its regulation of cellular energy expenditure (Hino S. Et al. Nat Commun. 2012, doi: 10.1038/ncomms1755), to its involvement in the control of checkpoints of viral gene expression in productive and latent infections (Roizman, B. J. Virol. 2011, 85, 7474-7482) and more specifically in the control of herpes virus infection (Gu, H. J. Virol. 2009, 83, 4376-4385) and HIV transcription (Sakane, N. et al. PLoS Pathog. 2011, 7(8):e1002184). The role of KDM1A in the regulation of neural stem cell proliferation (Sun, G. et al. Mol. Cell Biol. 2010, 30, 1997-2005) as well as in the control of neuritis morphogenesis (Zibetti, C. et al. J. Neurosci. 2010, 30, 2521-2532) suggest its possible involvement for neurodegenerative diseases.
Furthermore, there are evidences of the relevance of KDM1A in the control of other important cellular processes, such as DNA methylation (Wang, J. et al. Nat. Genet. 2009, 41(1):125-129), cell proliferation (Scoumanne, A. et al. J. Biol. Chem. 2007, 282, 15471-15475; Cho, H. S. et al. Cancer Res. 2011, 71, 655-660), epithelial mesenchimal transition (Lin, T. et al. Oncogene. 2010, 29, 4896-4904), and chromosome segregation (Lv, S. et al. Eur. J. Cell Biol. 2010, 89, 557-563). Moreover, several inhibitors of KDM1A have been identified in the last years and it was found that KDM1A inhibitors were able to reactivate silenced tumor suppressor genes (Huang, Y. et al. Proc. Natl. Acad. Sci. USA. 2007, 104, 8023-8028; Huang, Y. et al. Clin. Cancer Res. 2009, 15, 7217-7228), to target selectively cancer cells with pluripotent stem cells properties (Wang, J. et al. Cancer Res. 2011, 71, 7238-7249), as well as to reactivate the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia (Schenk, T. et al. Nat Med. 2012, 18, 605-611).
The more recently discovered demethylase KDM1B (LSD2) displays—similarly to KDM1A—specificity for mono- and di-methylated Lys4 of histone H3. KDM1B, differently from KDM1A, does not bind CoREST and it has not been found up to now in any of KDM1A-containing protein complex (Karytinos, A. et al. J. Biol. Chem. 2009, 284, 17775-17782). On the contrary, KDM1B forms active complexes with euchromatic histone methyltransferases G9a and NSD3 as well as with cellular factors involved in transcription elongation. In agreement, KDM1B has been reported to have a role as regulator of transcription elongation rather than that of a transcriptional repressor as proposed for KDM1A (Fang, R. et al. Mol. Cell 2010, 39, 222-233).
KDM1A and KDM1B are both flavo amino oxidases dependent proteins sharing a FAD coenzyme-binding motif, a SWIRM domain and an amine oxidase domain, all of which are integral to the enzymatic activity of KDM1 family members. Moreover, both KDM1A and KDM1B show a structural similarity with the monoamine oxidases MAO-A and MAO-B.
Indeed, tranylcypromine, a MAO inhibitor used as antidepressive agent, was found to be also able to inhibit LSD1. The compound acts as an irreversible inhibitor forming a covalent adduct with the FAD cofactor. (Lee, M. G. et al. Chem. Biol. 2006, 13, 563; Schmidt, D. M. Z. et al. Biochemistry 2007, 46, 4408).
The synthesis of tranylcypromine analogs and their LSD1 inhibitory activity has been described by Gooden, D. M. et al. in Bioorg. Med. Chem. Lett. 2008, 18, 3047-3051 and by Benelkebir, H. et al. in Bioorg. Med. Chem. 2011, 19, 3709-3716. Further arylcyclopropylamine and heteroarylcyclopropylamine derivatives as LSD1, MAO-A and/or MAO-B enzyme inhibitors are disclosed in US2010/324147, WO2012/013727 and in WO2012/045883.
Oryzon Genomics S. A. disclosed in WO2010/043721, WO2010/084160, WO2011/035941, WO2011/042217, and in WO2012/013728, cyclopropylaminoalkylamides, N-heterocyclyl-, aryl-, or heteroarylalkylcyclopropylamines with LSD1, MAO-A and/or MAO-B inhibitory activity, however no example of 2-aryl or heteroarylcyclopropylamine derivative substituted in position 1 of the cyclopropyl have been disclosed.
Further cyclopropylamines with LSD1 inhibitory activity and with the following general formula have been disclosed in WO2013/057320 and WO2013/057322:
wherein RW, RX, RY, and RZ are independently selected from hydrogen, fluoro and C1-4 alkyl, preferably from hydrogen, fluoro and methyl. A more preferred embodiment of the inventions are compounds, wherein RZ is hydrogen. No specific compound with RZ other than hydrogen has been disclosed in the two PCT patent applications.
GB950388 discloses phenylcyclopropylamine derivatives as monoamine oxidase inhibitors of following formula:
with R1 and R2 hydrogen or methyl having anorectic and antidepressant activity. WO1996/40126 describes 1H-4(5)-substituted imidazole derivatives having H3 histamine receptor agonist activity being useful in the treatment of diseases such as allergy, inflammation, cardio or cerebrovascular disease, gastrointestinal disorders and CNS disorders involving psychiatric disorders.
Substituted 1-methyl-2-phenyl- or 1-ethyl-2-phenylcyclopropylamine derivatives are described in WO2007/134799 as intermediates for the synthesis of macrobiocide derivatives. Additional cyclopropylamines substituted in position 1 are described by Patel, A. R. Acta Chem. Scand., 1966, 1424-1426, by Huisgen, R. et al. Chem. Berichte, 1972, 1324-1339, by Bertus, P. et al. Chem. Commun. (Camb.), 2001, 18, 1792-1793, by Shintani, R. et al. Chem. Commun. (Camb.), 2011, 47, 3057-3059, and Osipova, A. PhD “Synthesis of Diverse Polyfunctional Amides as Precursors to Potentially Interesting Peptidomimetics” Thesis Göttingen 2006.
The present invention relates to substituted cyclopropylamine derivatives having highly potent inhibitory activities of the KDM1A enzyme and/or of the KDM1B enzyme and low inhibitory activity of monoamine oxidases (MAOs), useful in the prevention or therapy of diseases and conditions associated with the activity of the histone demethylases. MAOs are well known targets for the treatment of diseases of the central nervous system, such as depression or Parkinson's disease. However, inhibition of the MAOs are associated with side effects, among them tyramine-induced hypertensive crisis or the serotonin syndrome, which occurs in situation of concomintant use of MAO inhibitors and other serotoninergic drugs. (Wimbiscus, M. et al. Cleve. Clin. J. Med., 2010, 859-882; Iqbal, M. M. Ann. Clin. Psychiatry, 2012, 24, 310-318).